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- PDB-1ee1: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -

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Basic information

Entry
Database: PDB / ID: 1ee1
TitleCRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION
ComponentsNH(3)-DEPENDENT NAD(+) SYNTHETASE
KeywordsLIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
NH(3)-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NICOTINIC ACID ADENINE DINUCLEOTIDE / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.06 Å
AuthorsDevedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / Delucas, L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Authors: Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / DeLucas, L.
#1: Journal: AM.CRYST.ASSOC.,ABSTR.PAPERS (SUMMER MEETING) / Year: 1997
Title: Asymmetric Complex of NAD+ Synthetase with Natural Substrates ATP Deamido-NAD+
Authors: Devedjiev, Y. / Singh, R. / Brouillette, C. / Muccio, D. / Brouillette, W. / DeLucas, L. / Jedzejas, M.
#2: Journal: AM.CRYST.ASSOC.,ABSTR.PAPERS (SUMMER MEETING) / Year: 1998
Title: Catalytic Cycle of NAD+ Synthetase Viewed by X-Ray Structures of Kinetic Intermediates
Authors: Devedjiev, Y. / Singh, R. / Brouillette, C. / Muccio, D. / Brouillette, W. / DeLucas, L. / Jedzejas, M.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NH(3)-DEPENDENT NAD(+) SYNTHETASE
B: NH(3)-DEPENDENT NAD(+) SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4706
Polymers60,6082
Non-polymers1,8624
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-63 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.98, 86.69, 60.48
Angle α, β, γ (deg.)90.0, 111.18, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NH(3)-DEPENDENT NAD(+) SYNTHETASE / NAD(+) SYNTHETASE


Mass: 30303.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: NADE / Production host: Escherichia coli (E. coli)
References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: PEG400, sodium acetate, magnesium chloride, adenosine triphosphate, deamido-NAD+, pH 5.2, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium acetate1drop
250 mM1dropMgCl2
32.5 mMbeta-mercaptoethanol1drop
415 mg/mlprotein1drop
521-23 %(v/v)PEG4001reservoir
60.1 Msodium acetate1reservoir
750 mM1reservoirMgCl2
85 mMNaAD1reservoir
90.5 mMATP1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 20, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. all: 98810 / Num. obs: 33464 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.156 / Num. unique all: 2584 / % possible all: 82.6
Reflection
*PLUS
Num. obs: 30068 / % possible obs: 95.4 % / Num. measured all: 136657 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 83 % / Mean I/σ(I) obs: 7.8

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Processing

Software
NameClassification
X-PLORrefinement
SCALEPACKdata scaling
RefinementResolution: 2.06→6 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: Used weighted least squares procedure. ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE ...Details: Used weighted least squares procedure. ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THE NICOTINIC ACID MOIETY OF DEAMIDO-NAD BOUND TO SUBUNIT B IS DISORDERED AS WELL, THOUGH THE REMAINDER OF THE SUBSTRATE IS WELL ORDERED. COORDINATES OF THE NICOTINIC ACID MOIETY IN SUBUNIT B ARE PRESENTED FOR REFERENCE. ATP BINDING SITE IN SUBUNIT A IS FULLY OCCUPIED, HOWEVER, NO BINDING OF ATP AND MG2+ WAS FOUND IN SUBUNIT B.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1240 -RANDOM
Rwork0.154 ---
all0.154 28724 --
obs0.154 23848 95 %-
Refinement stepCycle: LAST / Resolution: 2.06→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 120 397 4585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2.07
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 29684 / σ(F): 1 / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.2

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